The files include a transcriptome (FASTA format) and the following 8 genomic interval files (BED format):

Oly_snps_bed: location of SNPs with variant annotated in the name columnOly_geneID_bed: these intervals cover the entire length of the transcript and are annoated with the SwissProt ID in the name columnOly_regionofblasthits_bed: these intervals cover only the region of homology between the subject and query for the blastx outputOly_inducible_bed: these intervals cover the entire length of the transcript for those genes associated with the following GOSlim IDs: cell-cell signaling, signal transduction, cell adhesion, development, stress responseOly_housekeeping_bed: these intervals cover the entire length of the transcript for those genes associated with the following GOSlim IDs: DNA metabolism, RNA metabolism, protein metabolismOly_EcoRIsites_bed: location of EcoRI restriction sitesOly_NotIsites_bed: location of NotI restriction sitesOly_SbfI_bed: location of SbfI restriction sites

This dataset was generated as part of the requirements for FISH 546: Bioinformatics for Environmental Science. The slides for the final presentation are included (FISH546.pdf)

Oyster Tumbler

oystergen.es

Exploring the biology of oysters, a few hundred base pairs at at time.

This site is intended to serve as a portal for sharing research data, resources, and information as it pertains to active research efforts that intersect the fields of shellfish genomics and environmental science. The site currently highlights twospecies, a photo album, and a blog.

Some of the material on this site is based upon work supported by the National Science Foundation under Grant Number 1158119.

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation

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